Article
Biochemical Research Methods
Yen-Wen Wang, Cecile Ane
Summary: In this study, the authors present a kinship estimator called KIMGENS, which is capable of estimating kinship among individuals with various ploidies and is robust to population structure. The results show that KIMGENS outperforms previous estimators in accurately estimating kinship in simulated panmictic, structured, and admixed populations.
Review
Genetics & Heredity
Evan L. Sticca, Gillian M. Belbin, Christopher R. Gignoux
Summary: Identity-by-descent (IBD) is a fundamental concept in genomics, and recent methodological advances have enabled IBD detection in datasets containing millions of individuals, allowing for novel analyses at an unprecedented scale.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Jesse Smith, Ying Qiao, Amy L. Williams
Summary: This study examines the potential of using identity-by-descent segment numbers to improve relatedness inference. The researchers found that including segment numbers can increase recall rates for relatives, but current detection methods have limitations that dampen the signals in practice.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Jan-Niklas Runge, Barbara Konig, Anna K. Lindholm, Andres Bendesky
Summary: Genealogical relationships are important for genetic studies, but inferring correct pedigrees can be challenging even with genome-wide information. Inbreeding and genotyping errors are major factors that make pedigree inference difficult, especially in populations with high inbreeding or genotyping errors. This study introduces a new method called spore for inferring parent-offspring relationships in inbred pedigrees. Compared to existing methods, spore is superior at detecting parent-offspring relationships, particularly in the presence of inbreeding or genotyping errors.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Krishnanand P. Kulkarni, Nicholi Vorsa, Purushothaman Natarajan, Sathya Elavarthi, Massimo Iorizzo, Umesh K. Reddy, Kalpalatha Melmaiee
Summary: Genetic and admixture analysis of blueberry genotypes revealed wide genetic differentiation between Northern Highbush (NHB) and Southern Highbush (SHB) cultivars, with SHB cultivars showing higher genetic diversity. The study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism markers in genetic and admixture analyses, which can be useful for future breeding plans in blueberry.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Sam Tallman, Maria das Dores Sungo, Silvio Saranga, Sandra Beleza
Summary: This study presents a collection of 350 whole genome sequences from Angola and Mozambique, providing insights into significant demographic events in African history and shedding light on the complexity of the Bantu Expansion. The generated reference panels improve imputation accuracy in African Americans and Brazilians.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Maike L. Morrison, Nicolas Alcala, Noah A. Rosenberg
Summary: In model-based inference of population structure, individuals are assigned membership coefficients in statistical clusters generated by clustering algorithms. Different groups of individuals can have distinct patterns of variability in their membership coefficients, which are difficult to capture using a single numerical value. We introduce a method that measures the variability of membership coefficients in a predefined group, using an analogy between individual membership coefficient vectors and population allele frequency vectors. Our approach makes use of a normalized F-ST statistic and can be used to compare and analyze inferred population structures.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Alejandro Ochoa, John D. Storey
Summary: Kinship coefficients and F-ST are key parameters in modern population genetics studies, but existing estimators are biased due to restrictive assumptions when real datasets are considered. This study found that existing estimators can lead to severe biases and proposed a new estimation framework that is practically unbiased for any population structure. The new approach, demonstrated through theory and simulations, has the potential to significantly improve downstream analyses requiring accurate kinship and F-ST estimates.
Article
Agronomy
Phanchita Vejchasarn, Jeremy R. Shearman, Usawadee Chaiprom, Yotwarit Phansenee, Arissara Suthanthangjai, Jirapong Jairin, Varapong Chamarerk, Tatpong Tulyananda, Chainarong Amornbunchornvej
Summary: The study identified five subpopulations in the population structure of Thai rice, grouping individuals based on location. Each subpopulation exhibits unique genetic patterns, agronomic traits, and environmental conditions. This research can serve as a valuable reference for breeders and researchers interested in Thai rice.
Article
Multidisciplinary Sciences
Elena Arciero, Sufyan A. Dogra, Daniel S. Malawsky, Massimo Mezzavilla, Theofanis Tsismentzoglou, Qin Qin Huang, Karen A. Hunt, Dan Mason, Saghira Malik Sharif, David A. van Heel, Eamonn Sheridan, John Wright, Neil Small, Shai Carmi, Mark M. Iles, Hilary C. Martin
Summary: The research uncovered a strong recent population structure among British Pakistanis, influenced by the Biraderi social stratification system. All subgroups had low recent effective population sizes, with extensive identity-by-descent sharing and homozygosity increasing the risk of recessive disorders. The impact of cultural practices on Pakistani population structure and genomic diversity was highlighted, with implications for medical genetic studies.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Tam Minh Nguyen, Duy Dinh Vu, Hien Phan Dang, Xuan Thi Tuyet Bui, Hong Phan Lan Nguyen, Duc Minh Nguyen
Summary: Moderate levels of genetic diversity and differentiation were found in Anisoptera costata. Population divergence during the Younger Dryas was detected. The anthropogenic disturbance significantly impacted the genetic diversity of the species in low tropical forests.
Article
Biochemical Research Methods
Alissa L. Severson, Thorfinn Sand Korneliussen, Ida Moltke
Summary: In this study, a new probabilistic software tool called LocalNgsRelate is proposed for inferring identity-by-descent (IBD) sharing along the genome between pairs of individuals from low-depth Next Generation Sequencing (NGS) data. The method takes the uncertainty of genotype calling into account, leading to more accurate inference compared to existing methods. It is also shown to work well for NGS data down to a depth of 2x.
Article
Biochemistry & Molecular Biology
Laurence Gagnon, Claudia Moreau, Catherine Laprise, Helene Vezina, Simon L. Girard
Summary: Using genealogy, researchers studied the demographic history of Quebec's population over the last 400 years. The study showed that the Quebec population structure began forming in the St. Lawrence valley as early as 1750, with distinct groups like the Saguenay and Gaspesian groups. Ancestors of these groups experienced increased kinship and inbreeding levels, leading to the contemporary population structure. Regional founder effects resulted in differences in genetic sharing among these groups, with Gaspe and North Shore groups sharing more large segments and the Sagueneans sharing more short segments.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Agriculture, Dairy & Animal Science
Sonia Bedhiaf-Romdhani, Imen Baazaoui, Ken G. Dodds, Rudiger Brauning, Rayna M. Anderson, Tracey C. Van Stijn, Alan F. McCulloch, John Colin McEwan
Summary: In developing countries, molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique is an efficient method for simultaneous discovery and genotyping of many markers. In this study, a GBS protocol was applied to discover SNP markers among Tunisian sheep samples, leading to the identification of potential genes related to sheep tail-type traits and providing insights into sheep adaptation to arid areas. GBS could be a valuable tool in livestock species in developing/emerging countries.
Article
Biochemistry & Molecular Biology
Kylie M. Cairns, Mathew S. Crowther, Heidi G. Parker, Elaine A. Ostrander, Mike Letnic
Summary: Admixture between canid species is a concern in wildlife management. By genotyping 402 wild dingoes and comparing them with domestic dogs using SNP genotyping, the study reveals at least five distinct dingo populations in Australia and limited evidence of dog admixture in wild dingoes. These findings challenge previous reports and support the use of genome-wide SNP genotyping to inform dingo management policy and legislation.